How gene order is influenced by the biophysics of transcription regulation

Abstract

What are the forces that shape the structure of prokaryotic genomes: the order of genes, their proximity, and their orientation? Coregulation and coordinated horizontal gene transfer are believed to promote the proximity of functionally related genes and the formation of operons. However, forces that influence the structure of the genome beyond the level of a single operon remain unknown. Here, we show that the biophysical mechanism by which regulatory proteins search for their sites on DNA can impose constraints on genome structure. Using simulations, we demonstrate that rapid and reliable gene regulation requires that the transcription factor (TF) gene be close to the site on DNA the TF has to bind, thus promoting the colocalization of TF genes and their targets on the genome. We use parameters that have been measured in recent experiments to estimate the relevant length and times scales of this process and demonstrate that the search for a cognate site may be prohibitively slow if a TF has a low copy number and is not colocalized. We also analyze TFs and their sites in a number of bacterial genomes, confirm that they are colocalized significantly more often than expected, and show that this observation cannot be attributed to the pressure for coregulation or formation of selfish gene clusters, thus supporting the role of the biophysical constraint in shaping the structure of prokaryotic genomes. Our results demonstrate how spatial organization can influence timing and noise in gene expression.diffusion ͉ genetics ͉ genomics ͉ protein-DNA interactions ͉ spatial effects T he colocalization of prokaryotic transcription factor (TF) genes and their binding sites is known from the pioneering work of Jacob and Monod (1) on the lactose operon and has been shown to be widespread (2-4) and essential for the formation of regulatory motifs (5). Some have hypothesized that TF-binding site colocalization is advantageous, in part, because it could expedite a TF's search for its site (2, 5-7) (the rapid search hypothesis). In prokaryotes, this speed-up by colocalization is possible because transcription and translation are coupled spatially and temporally. Therefore, TFs are synthesized near their genes and can rapidly bind colocalized sites (Fig. 1A). The arrival time of a TF to its site ultimately controls the timing of gene regulation, whereas fluctuations in the arrival time can lead to bursts of gene activity and noise in gene regulation. The rapid search hypothesis suggests that colocalization is favorable because expediting TF arrival makes regulation faster and more reliable.Both experimentally (see ref.8 for an overview) and theoretically (9-13), many have studied the broader question: how can a TF find its cognate site on DNA among Ϸ10 7 decoy sites in a fraction of a minute while moving in the crowded environment of the cell and hampered by other DNA-bound proteins? The general model of the process includes 3D spatial diffusion of the TF through the cell volume and 1D sliding of a TF along DNA. According to this m...

Probing microscopic origins of confined subdiffusion by first-passage observables

“…Indeed, in the cases where the fractal description of the cell environment is relevant, our results show that reaction times crucially depend on the sourcetarget distance r. The biological importance of such dependence on the starting point was recently emphasized in ref. 39 on the example of gene colocalization. However, when the CTRW description of transport is valid, reaction times do not depend on the starting point at large distance r. (ii) The splitting probabilities for the CTRW model and for the fractal models have different scalings with the distance between the source and the targets.…”

“…This quantity is fundamental in the study of transportlimited reactions (31)(32)(33), because it gives the reaction time in the limit of perfect reaction. This quantity is also useful in target search problems (34)(35)(36)(37)(38)(39) and other physical systems (40)(41)(42). We will be interested in both the probability density function (PDF) of the FPT, and its first moment, the mean FPT (MFPT).…”

Facilitated diffusion with DNA coiling

“…Such proteins thereby transfer across a point of close contact without actually leaving the DNA (5). Facilitated diffusion has recently received renewed interest, following a variety of new conceptual viewpoints of gene regulation (13)(14)(15)(16)(17)(18). Fresh impetus has also been given by the possibility to monitor the target search by DNA-binding proteins on the level of single DNA molecules.…”

Az anyagcsere szerkezetének hatása a genetikai interakciókra és a genomszerveződésre

“…A hasonló funkciójú fehérjéket kódoló gének, ha nem is pontosan azonos sorrendben maradnak meg, de a kromoszómán csoportokba tömörülve, egymás mellett, vagy közelében fordulnak elő (Rogozin et al, 2002;Yang and Sze, 2008;Ling et al, 2009). Ezt a nagyobb léptékben konzervált szerveződést über-operon 15 -nak is nevezik (Lathe et al, 2000) Hasonló funkciójú gének operonokon felüli csoportokba rendeződésére legismertebb egyedi példák a riboszomális fehérjék szuperoperonja (Reams and Neidle, 2004) vagy a horizontális transzferhez köthető "genomi szigetek" (Hacker and Carniel, 2001) (Kolesov et al, 2007;Janga et al, 2009). Azt, hogy az ilyen géncsoportok léte a transzkripciós faktor hatékonyabb célbajuttatására ható szelekció eredménye lehet (ún.…”

“…Azt, hogy az ilyen géncsoportok léte a transzkripciós faktor hatékonyabb célbajuttatására ható szelekció eredménye lehet (ún. "rapid search hypothesis"), alátámasztja az is, hogy a transzkripciós faktor génje és a célgén egyirányú orientációt mutat, amely minimalizálja a fizikai távolságot a képződő transzkripciós faktor és a célgén promótere között (Kolesov et al, 2007).…”